From: Adam Liwo Date: Tue, 29 May 2012 08:52:17 +0000 (-0400) Subject: 5/29/2012 by Adam X-Git-Tag: v.3.2~80^2~11^2~9 X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=bc8826038ee36f9d7f1d6dd89c90601b2562c0af 5/29/2012 by Adam 1. Fixed NaNs in wham (more stable computation of window free energies). 2. Minor fixes in cluster 3. Added exmaple with minimization in MD examples --- diff --git a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe index 70fd7a9..7e3eb18 100755 Binary files a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe and b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe differ diff --git a/bin/wham/wham_ifort_MPICH_E0LL2Y.exe b/bin/wham/wham_ifort_MPICH_E0LL2Y.exe index 90bd886..508b4f6 100755 Binary files a/bin/wham/wham_ifort_MPICH_E0LL2Y.exe and b/bin/wham/wham_ifort_MPICH_E0LL2Y.exe differ diff --git a/bin/wham/wham_ifort_MPICH_GAB.exe b/bin/wham/wham_ifort_MPICH_GAB.exe index 4ac1bc2..3b52754 100755 Binary files a/bin/wham/wham_ifort_MPICH_GAB.exe and b/bin/wham/wham_ifort_MPICH_GAB.exe differ diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.inp b/examples/unres/MD/ff_gab/1L2Y_minim.inp index 286b667..2830886 100644 --- a/examples/unres/MD/ff_gab/1L2Y_minim.inp +++ b/examples/unres/MD/ff_gab/1L2Y_minim.inp @@ -1,6 +1,6 @@ 1L2Y -SEED=-3059743 PDBREF MINIMIZE -maxmin=1000 +SEED=-3059743 REFSTR PDBREF MINIMIZE + WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 & WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 & WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 & diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.intin b/examples/unres/MD/ff_gab/1L2Y_minim.intin new file mode 100644 index 0000000..e69de29 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.out_GB b/examples/unres/MD/ff_gab/1L2Y_minim.out_GB new file mode 100644 index 0000000..18ee121 --- /dev/null +++ b/examples/unres/MD/ff_gab/1L2Y_minim.out_GB @@ -0,0 +1,471 @@ +-------------------------------------------------------------------------------- + FILE ASSIGNMENT +-------------------------------------------------------------------------------- + Input file : 1L2Y_minim.inp + Output file : 1L2Y_minim.out_GB + + Sidechain potential file : + ../../../../PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k + SCp potential file : ../../../../PARAM/scp.parm + Electrostatic potential file : ../../../../PARAM/electr_631Gdp.parm + Cumulant coefficient file : + ../../../../PARAM/fourier_opt.parm.1igd_hc_iter3_3 + Torsional parameter file : ../../../../PARAM/torsion_631Gdp.parm + Double torsional parameter file : ../../../../PARAM/torsion_double_631Gdp.parm + SCCOR parameter file : ../../../../PARAM/rotcorr_AM1.parm + Bond & inertia constant file : ../../../../PARAM/bond.parm + Bending parameter file : ../../../../PARAM/thetaml.5parm + Rotamer parameter file : ../../../../PARAM/scgauss.parm + Threading database : ../../../../PARAM/patterns.cart +-------------------------------------------------------------------------------- + ### LAST MODIFIED 03/28/12 23:29 by czarek + ++++ Compile info ++++ + Version 2.5 build 34 + compiled Mon Apr 2 08:16:44 2012 + compiled by adam@matrix.chem.cornell.edu + OS name: Linux + OS release: 2.6.34.9-69.fc13.x86_64 + OS version: #1 SMP Tue May 3 09:23:03 UTC 2011 + flags: + FC = ifort + FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include + FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)... + FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include + FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ... + CC = cc + CFLAGS = -DLINUX -DPGI -c + OPT = -O3 -ip -w + LIBS = -Lxdrf -lxdrf + ARCH = LINUX + PP = /lib/cpp -P + object = unres.o arcos.o cartprint.o chainbuild... + GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ... + GAB: BIN = ../../../bin/unres/MD/unres_ifort_si... + E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR... + E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort... + ++++ End of compile info ++++ + +Potential is GB , exponents are 6 12 + +Disulfide bridge parameters: +S-S bridge energy: -5.50 +d0cm: 3.78 akcm: 15.10 +akth: 11.00 akct: 12.00 +v1ss: -1.08 v2ss: 7.61 v3ss: 13.70 + ran_num 0.930227314089531 +RMSDBC = 3.0 +RMSDBC1 = 0.5 +RMSDBC1MAX = 1.5 +DRMS = 0.1 +RMSDBCM = 3.0 +Time limit (min): 960.0 + RESCALE_MODE 1 +Library routine used to diagonalize matrices. + +******************************************************************************** + Options in energy minimization: +******************************************************************************** +MaxMin: 2000 MaxFun: 5000MinMin: 2000 MinFun: 2000 TolF: 1.00000E-02 RTolF: 1.00000E-04 + +Energy-term weights (unscaled): + +WSCC= 1.352790 (SC-SC) +WSCP= 1.593040 (SC-p) +WELEC= 0.715340 (p-p electr) +WVDWPP= 0.113710 (p-p VDW) +WBOND= 1.000000 (stretching) +WANG= 1.138730 (bending) +WSCLOC= 0.162580 (SC local) +WTOR= 1.985990 (torsional) +WTORD= 1.570690 (double torsional) +WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) +WEL_LOC= 0.160360 (multi-body 3-rd order) +WCORR4= 0.428870 (multi-body 4th order) +WCORR5= 0.000000 (multi-body 5th order) +WCORR6= 0.000000 (multi-body 6th order) +WSCCOR= 0.000000 (back-scloc correlation) +WTURN3= 1.687220 (turns, 3rd order) +WTURN4= 0.662300 (turns, 4th order) +WTURN6= 0.000000 (turns, 6th order) + +Hydrogen-bonding correlation between contact pairs of peptide groups + +Scaling factor of 1,4 SC-p interactions: 0.400 +General scaling factor of SC-p interactions: 1.000 + +Energy-term weights (scaled): + +WSCC= 1.352790 (SC-SC) +WSCP= 1.593040 (SC-p) +WELEC= 0.715340 (p-p electr) +WVDWPP= 0.113710 (p-p VDW) +WBOND= 1.000000 (stretching) +WANG= 1.138730 (bending) +WSCLOC= 0.162580 (SC local) +WTOR= 1.985990 (torsional) +WTORD= 1.570690 (double torsional) +WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) +WEL_LOC= 0.160360 (multi-body 3-rd order) +WCORR4= 0.428870 (multi-body 4th order) +WCORR5= 0.000000 (multi-body 5th order) +WCORR6= 0.000000 (multi-body 6th order) +WSCCOR= 0.000000 (back-scloc correlatkion) +WTURN3= 1.687220 (turns, 3rd order) +WTURN4= 0.662300 (turns, 4th order) +WTURN6= 0.000000 (turns, 6th order) + Reference temperature for weights calculation: 300.000000000000 + Parameters of the SS-bond potential: + D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH + 11.0000000000000 AKCT 12.0000000000000 + V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS + 13.7000000000000 + EBR -5.50000000000000 +PDB data will be read from file 1L2Y.pdb + Nres: 21 +Backbone and SC coordinates as read from the PDB + 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051 + 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437 + 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850 + 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797 + 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074 + 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853 + 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450 + 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799 + 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146 + 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676 + 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593 + 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723 + 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058 + 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675 + 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546 + 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870 + 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986 + 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688 + 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856 + 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430 + 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488 + 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754 +nsup= 20 nstart_sup= 2 + ITEL + 1 21 0 + 2 14 1 + 3 5 1 + 4 8 1 + 5 4 1 + 6 13 1 + 7 7 1 + 8 5 1 + 9 19 1 + 10 16 1 + 11 10 1 + 12 10 2 + 13 20 1 + 14 12 1 + 15 12 1 + 16 10 1 + 17 18 2 + 18 20 2 + 19 20 2 + 20 20 1 + 21 12 0 + ns= 0 iss: +Boundaries in phi angle sampling: +D 1 -180.0 180.0 +ASN 2 -180.0 180.0 +LEU 3 -180.0 180.0 +TYR 4 -180.0 180.0 +ILE 5 -180.0 180.0 +GLN 6 -180.0 180.0 +TRP 7 -180.0 180.0 +LEU 8 -180.0 180.0 +LYS 9 -180.0 180.0 +ASP 10 -180.0 180.0 +GLY 11 -180.0 180.0 +GLY 12 -180.0 180.0 +PRO 13 -180.0 180.0 +SER 14 -180.0 180.0 +SER 15 -180.0 180.0 +GLY 16 -180.0 180.0 +ARG 17 -180.0 180.0 +PRO 18 -180.0 180.0 +PRO 19 -180.0 180.0 +PRO 20 -180.0 180.0 +SER 21 -180.0 180.0 +D 22 -180.0 180.0 +nsup= 20 + nsup= 20 nstart_sup= 2 nstart_seq= 2 + NZ_START= 2 NZ_END= 21 + IZ_SC= 0 + Contact order: 0.308441558441558 + Shifting contacts: 2 2 + 1 ILE 5 ASN 2 + 2 TRP 7 TYR 4 + 3 LEU 8 TYR 4 + 4 LEU 8 ILE 5 + 5 LYS 9 GLN 6 + 6 GLY 12 TRP 7 + 7 GLY 12 LEU 8 + 8 SER 14 GLY 11 + 9 SER 15 ASP 10 + 10 SER 15 GLY 11 + 11 PRO 19 TRP 7 + 12 PRO 20 LEU 3 + 13 PRO 20 TYR 4 + 14 PRO 20 TRP 7 +Initial geometry will be read in. + +Geometry of the virtual chain. + Res d Theta Gamma Dsc Alpha Beta +D 1 0.000 0.000 0.000 0.000 0.000 0.000 +ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317 +LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685 +TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090 +ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666 +GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945 +TRP 7 3.800 84.466 51.434 2.605 152.178 38.024 +LEU 8 3.800 83.945 53.508 1.939 159.052 179.471 +LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090 +ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797 +GLY 11 3.800 94.602 67.604 0.000 0.000 0.000 +GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000 +PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163 +SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659 +SER 15 3.800 96.264 67.358 1.150 146.290 -130.305 +GLY 16 3.800 138.119 129.701 0.000 0.000 0.000 +ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747 +PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641 +PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044 +PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374 +SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303 +D 22 3.800 108.718 92.113 0.000 0.000 0.000 +Energy evaluation or minimization calculation. + +Conformations will be energy-minimized. +******************************************************************************** + + Time for energy evaluation 0.000000000000000E+000 + +Virtual-chain energies: + +EVDW= -4.954316E+01 WEIGHT= 1.352790D+00 (SC-SC) +EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p) +EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p) +EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW) +ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching) +EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending) +ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local) +ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional) +ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional) +EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) +ECORR4= -8.338619E+01 WEIGHT= 4.288700D-01 (multi-body) +ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +EELLO= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local) +ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order) +ETURN4= -7.304754E+00 WEIGHT= 6.623000D-01 (turns, 4th order) +ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) +ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr) +EDIHC= 0.000000E+00 (dihedral angle constraints) +ESS= 0.000000E+00 (disulfide-bridge intrinsic energy) +UCONST= 0.000000E+00 (Constraint energy) +ETOT= -5.845169E+01 (total) +PP contact map: + 1 ASN 2 TYR 4 + 2 ASN 2 ILE 5 + 3 LEU 3 ILE 5 + 4 LEU 3 GLN 6 + 5 TYR 4 GLN 6 + 6 TYR 4 TRP 7 + 7 TYR 4 LEU 8 + 8 ILE 5 TRP 7 + 9 ILE 5 LEU 8 + 10 GLN 6 LEU 8 + 11 GLN 6 LYS 9 + 12 TRP 7 LYS 9 + 13 TRP 7 ASP 10 + 14 TRP 7 GLY 11 + 15 TRP 7 GLY 12 + 16 LEU 8 ASP 10 + 17 LEU 8 GLY 11 + 18 LYS 9 GLY 11 + 19 ASP 10 GLY 12 + 20 GLY 11 PRO 13 + 21 GLY 11 SER 14 + 22 GLY 12 SER 14 + 23 SER 14 GLY 16 + 24 SER 15 ARG 17 + 25 GLY 16 PRO 18 + 26 ARG 17 PRO 19 + 27 PRO 18 PRO 20 + Hairpins: +Constants of electrostatic interaction energy expression. + 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01 + 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01 + Total average electrostatic energy: -17.0351458449875 + VDW energy between peptide-group centers: -10.2064531653452 + + Electrostatic contacts before pruning: + 1 ASN 2 TYR 4 -1.06027 + 2 LEU 3 ILE 5 -1.59865 + 3 LEU 3 GLN 6 -0.54360 + 4 TYR 4 GLN 6 -2.10033 + 5 TYR 4 TRP 7 -0.84900 + 6 ILE 5 TRP 7 -1.85979 + 7 ILE 5 LEU 8 -0.53540 + 8 GLN 6 LEU 8 -1.48363 + 9 GLN 6 LYS 9 -0.61868 + 10 TRP 7 LYS 9 -1.55464 + 11 TRP 7 GLY 12 -0.37651 + 12 LEU 8 ASP 10 -0.61626 + 13 LEU 8 GLY 11 -0.40662 + + Electrostatic contacts after pruning: + 1 ASN 2 TYR 4 -1.06027 + 2 LEU 3 ILE 5 -1.59865 + 3 LEU 3 GLN 6 -0.54360 + 4 TYR 4 GLN 6 -2.10033 + 5 TYR 4 TRP 7 -0.84900 + 6 ILE 5 TRP 7 -1.85979 + 7 ILE 5 LEU 8 -0.53540 + 8 GLN 6 LEU 8 -1.48363 + 9 GLN 6 LYS 9 -0.61868 + 10 TRP 7 LYS 9 -1.55464 + 11 TRP 7 GLY 12 -0.37651 + 12 LEU 8 ASP 10 -0.61626 + 13 LEU 8 GLY 11 -0.40662 +Helix 1 2 10 + UNRES seq: + helix 3 11 + SC_move 1190 -14.2312827671102 +PP contact map: + 1 ASN 2 TYR 4 + 2 ASN 2 ILE 5 + 3 LEU 3 ILE 5 + 4 LEU 3 GLN 6 + 5 LEU 3 TRP 7 + 6 TYR 4 GLN 6 + 7 TYR 4 TRP 7 + 8 TYR 4 LEU 8 + 9 ILE 5 TRP 7 + 10 ILE 5 LEU 8 + 11 ILE 5 LYS 9 + 12 GLN 6 LEU 8 + 13 GLN 6 LYS 9 + 14 TRP 7 LYS 9 + 15 TRP 7 ASP 10 + 16 TRP 7 GLY 11 + 17 TRP 7 GLY 12 + 18 LEU 8 ASP 10 + 19 LEU 8 GLY 11 + 20 LYS 9 GLY 11 + 21 ASP 10 GLY 12 + 22 GLY 11 PRO 13 + 23 GLY 11 SER 14 + 24 GLY 12 SER 14 + 25 PRO 13 SER 15 + 26 SER 14 GLY 16 + 27 SER 15 ARG 17 + 28 PRO 18 PRO 20 + Hairpins: +Constants of electrostatic interaction energy expression. + 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01 + 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01 + Total average electrostatic energy: -14.3281191505659 + VDW energy between peptide-group centers: -22.1278543766753 + + Electrostatic contacts before pruning: + 1 ASN 2 TYR 4 -0.80580 + 2 LEU 3 ILE 5 -1.08899 + 3 LEU 3 GLN 6 -0.51166 + 4 TYR 4 GLN 6 -1.35288 + 5 TYR 4 TRP 7 -0.71638 + 6 ILE 5 TRP 7 -1.25245 + 7 ILE 5 LEU 8 -0.56094 + 8 GLN 6 LEU 8 -1.12103 + 9 GLN 6 LYS 9 -0.52058 + 10 TRP 7 LYS 9 -1.15119 + 11 LEU 8 ASP 10 -0.71444 + 12 LEU 8 GLY 11 -0.38113 + 13 GLY 12 SER 14 -0.61187 + + Electrostatic contacts after pruning: + 1 ASN 2 TYR 4 -0.80580 + 2 LEU 3 ILE 5 -1.08899 + 3 LEU 3 GLN 6 -0.51166 + 4 TYR 4 GLN 6 -1.35288 + 5 TYR 4 TRP 7 -0.71638 + 6 ILE 5 TRP 7 -1.25245 + 7 ILE 5 LEU 8 -0.56094 + 8 GLN 6 LEU 8 -1.12103 + 9 GLN 6 LYS 9 -0.52058 + 10 TRP 7 LYS 9 -1.15119 + 11 LEU 8 ASP 10 -0.71444 + 12 LEU 8 GLY 11 -0.38113 + 13 GLY 12 SER 14 -0.61187 +Helix 1 2 10 + UNRES seq: + helix 3 11 + +Virtual-chain energies: + +EVDW= -5.340090E+01 WEIGHT= 1.352790D+00 (SC-SC) +EVDW2= 4.677947E+01 WEIGHT= 1.593040D+00 (SC-p) +EES= -9.503008E+01 WEIGHT= 7.153400D-01 (p-p) +EVDWPP= -2.608496E+01 WEIGHT= 1.137100D-01 (p-p VDW) +ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching) +EBE= -3.660091E+01 WEIGHT= 1.138730D+00 (bending) +ESC= 8.674390E+01 WEIGHT= 1.625800D-01 (SC local) +ETORS= 9.615105E+00 WEIGHT= 1.985990D+00 (torsional) +ETORSD= 4.819701E-01 WEIGHT= 1.570690D+00 (double torsional) +EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) +ECORR4= -7.040856E+01 WEIGHT= 4.288700D-01 (multi-body) +ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +EELLO= -7.334513E+00 WEIGHT= 1.603600D-01 (electrostatic-local) +ETURN3= 1.856553E+01 WEIGHT= 1.687220D+00 (turns, 3rd order) +ETURN4= -3.312436E+00 WEIGHT= 6.623000D-01 (turns, 4th order) +ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) +ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr) +EDIHC= 0.000000E+00 (dihedral angle constraints) +ESS= 0.000000E+00 (disulfide-bridge intrinsic energy) +UCONST= 0.000000E+00 (Constraint energy) +ETOT= -7.862875E+01 (total) + +Geometry of the virtual chain. + Res d Theta Gamma Dsc Alpha Beta +D 1 0.000 0.000 0.000 0.000 0.000 0.000 +ASN 2 3.800 0.000 0.000 1.684 110.702 -85.685 +LEU 3 3.800 118.494 0.000 1.939 141.228 -49.540 +TYR 4 3.800 91.717 -100.428 2.484 118.549 113.868 +ILE 5 3.800 90.036 63.646 1.776 146.652 -96.973 +GLN 6 3.800 89.040 55.793 2.240 104.893 -50.566 +TRP 7 3.800 90.433 45.276 2.605 138.711 59.219 +LEU 8 3.800 90.769 45.241 1.939 136.395 -145.480 +LYS 9 3.800 90.500 50.320 2.541 134.179 -136.318 +ASP 10 3.800 92.103 46.289 1.709 143.475 -124.446 +GLY 11 3.800 91.360 65.751 0.000 180.000 180.000 +GLY 12 3.800 111.681 -71.670 0.000 180.000 180.000 +PRO 13 3.800 113.684 -58.655 1.345 129.775 -154.011 +SER 14 3.800 93.263 -78.152 1.150 115.010 -77.057 +SER 15 3.800 93.932 57.849 1.150 124.898 -144.294 +GLY 16 3.800 115.865 137.415 0.000 180.000 180.000 +ARG 17 3.800 94.303 -84.359 3.020 90.176 -107.687 +PRO 18 3.800 121.756 61.635 1.345 116.339 -177.378 +PRO 19 3.800 117.856 -81.085 1.345 141.987 -158.715 +PRO 20 3.800 115.623 -108.327 1.345 97.877 -97.653 +SER 21 3.800 93.855 -137.450 1.150 144.130 -129.546 +D 22 3.800 117.793 46.049 0.000 180.000 180.000 +RMS deviation from the reference structure: 2.067 + % of native contacts: 78.571 + % of nonnative contacts: 54.167 + contact order: 0.348 +SUMSL return code: 4 +# of energy evaluations: 348 +# of energy evaluations/sec: 3154.545 + + +***** Computation time: 0 hours 0 minutes 0 seconds ***** diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.out_GB000 b/examples/unres/MD/ff_gab/1L2Y_minim.out_GB000 new file mode 100644 index 0000000..adbd935 --- /dev/null +++ b/examples/unres/MD/ff_gab/1L2Y_minim.out_GB000 @@ -0,0 +1,494 @@ +-------------------------------------------------------------------------------- + FILE ASSIGNMENT +-------------------------------------------------------------------------------- + Input file : 1L2Y_minim.inp + Output file : 1L2Y_minim.out_GB000 + + Sidechain potential file : + /users/adam/UNRES/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k + SCp potential file : /users/adam/UNRES/PARAM/scp.parm + Electrostatic potential file : /users/adam/UNRES/PARAM/electr_631Gdp.parm + Cumulant coefficient file : + /users/adam/UNRES/PARAM/fourier_opt.parm.1igd_hc_iter3_3 + Torsional parameter file : /users/adam/UNRES/PARAM/torsion_631Gdp.parm + Double torsional parameter file : + /users/adam/UNRES/PARAM/torsion_double_631Gdp.parm + SCCOR parameter file : /users/adam/UNRES/PARAM/rotcorr_AM1.parm + Bond & inertia constant file : /users/adam/UNRES/PARAM/bond.parm + Bending parameter file : /users/adam/UNRES/PARAM/thetaml.5parm + Rotamer parameter file : /users/adam/UNRES/PARAM/scgauss.parm + Threading database : /users/adam/UNRES/PARAM/patterns.cart +-------------------------------------------------------------------------------- +******************************************************************************** +United-residue force field calculation - parallel job. +******************************************************************************** + ### LAST MODIFIED 03/28/12 23:29 by czarek + ++++ Compile info ++++ + Version 2.5 build 62 + compiled Sun May 13 16:07:22 2012 + compiled by adam@matrix.chem.cornell.edu + OS name: Linux + OS release: 2.6.34.9-69.fc13.x86_64 + OS version: #1 SMP Tue May 3 09:23:03 UTC 2011 + flags: + INSTALL_DIR = /users/software/mpich-1.2.7p1_int... + FC= ifort + OPT = -O3 -ip -w + FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include + FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)... + FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include + FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ... + LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr... + ARCH = LINUX + PP = /lib/cpp -P + object = unres.o arcos.o cartprint.o chainbuild... + GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ... + GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP... + E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR... + E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort... + ++++ End of compile info ++++ + +Potential is GB , exponents are 6 12 + +Disulfide bridge parameters: +S-S bridge energy: -5.50 +d0cm: 3.78 akcm: 15.10 +akth: 11.00 akct: 12.00 +v1ss: -1.08 v2ss: 7.61 v3ss: 13.70 + MPI: node= 0 iseed(4)= 0 0 -46 + -45086 + ran_num 6.422640197456531E-013 +RMSDBC = 3.0 +RMSDBC1 = 0.5 +RMSDBC1MAX = 1.5 +DRMS = 0.1 +RMSDBCM = 3.0 +Time limit (min): 960.0 + RESCALE_MODE 1 +Library routine used to diagonalize matrices. + +******************************************************************************** + Options in energy minimization: +******************************************************************************** +MaxMin: 2000 MaxFun: 5000MinMin: 2000 MinFun: 2000 TolF: 1.00000E-02 RTolF: 1.00000E-04 + +Energy-term weights (unscaled): + +WSCC= 1.352790 (SC-SC) +WSCP= 1.593040 (SC-p) +WELEC= 0.715340 (p-p electr) +WVDWPP= 0.113710 (p-p VDW) +WBOND= 1.000000 (stretching) +WANG= 1.138730 (bending) +WSCLOC= 0.162580 (SC local) +WTOR= 1.985990 (torsional) +WTORD= 1.570690 (double torsional) +WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) +WEL_LOC= 0.160360 (multi-body 3-rd order) +WCORR4= 0.428870 (multi-body 4th order) +WCORR5= 0.000000 (multi-body 5th order) +WCORR6= 0.000000 (multi-body 6th order) +WSCCOR= 0.000000 (back-scloc correlation) +WTURN3= 1.687220 (turns, 3rd order) +WTURN4= 0.662300 (turns, 4th order) +WTURN6= 0.000000 (turns, 6th order) + +Hydrogen-bonding correlation between contact pairs of peptide groups + +Scaling factor of 1,4 SC-p interactions: 0.400 +General scaling factor of SC-p interactions: 1.000 + +Energy-term weights (scaled): + +WSCC= 1.352790 (SC-SC) +WSCP= 1.593040 (SC-p) +WELEC= 0.715340 (p-p electr) +WVDWPP= 0.113710 (p-p VDW) +WBOND= 1.000000 (stretching) +WANG= 1.138730 (bending) +WSCLOC= 0.162580 (SC local) +WTOR= 1.985990 (torsional) +WTORD= 1.570690 (double torsional) +WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) +WEL_LOC= 0.160360 (multi-body 3-rd order) +WCORR4= 0.428870 (multi-body 4th order) +WCORR5= 0.000000 (multi-body 5th order) +WCORR6= 0.000000 (multi-body 6th order) +WSCCOR= 0.000000 (back-scloc correlatkion) +WTURN3= 1.687220 (turns, 3rd order) +WTURN4= 0.662300 (turns, 4th order) +WTURN6= 0.000000 (turns, 6th order) + Reference temperature for weights calculation: 300.000000000000 + Parameters of the SS-bond potential: + D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH + 11.0000000000000 AKCT 12.0000000000000 + V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS + 13.7000000000000 + EBR -5.50000000000000 +PDB data will be read from file 1L2Y.pdb + Nres: 21 +Backbone and SC coordinates as read from the PDB + 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051 + 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437 + 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850 + 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797 + 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074 + 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853 + 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450 + 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799 + 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146 + 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676 + 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593 + 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723 + 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058 + 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675 + 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546 + 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870 + 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986 + 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688 + 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856 + 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430 + 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488 + 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754 +nsup= 20 nstart_sup= 2 + ITEL + 1 21 0 + 2 14 1 + 3 5 1 + 4 8 1 + 5 4 1 + 6 13 1 + 7 7 1 + 8 5 1 + 9 19 1 + 10 16 1 + 11 10 1 + 12 10 2 + 13 20 1 + 14 12 1 + 15 12 1 + 16 10 1 + 17 18 2 + 18 20 2 + 19 20 2 + 20 20 1 + 21 12 0 + ns= 0 iss: +Boundaries in phi angle sampling: +D 1 -180.0 180.0 +ASN 2 -180.0 180.0 +LEU 3 -180.0 180.0 +TYR 4 -180.0 180.0 +ILE 5 -180.0 180.0 +GLN 6 -180.0 180.0 +TRP 7 -180.0 180.0 +LEU 8 -180.0 180.0 +LYS 9 -180.0 180.0 +ASP 10 -180.0 180.0 +GLY 11 -180.0 180.0 +GLY 12 -180.0 180.0 +PRO 13 -180.0 180.0 +SER 14 -180.0 180.0 +SER 15 -180.0 180.0 +GLY 16 -180.0 180.0 +ARG 17 -180.0 180.0 +PRO 18 -180.0 180.0 +PRO 19 -180.0 180.0 +PRO 20 -180.0 180.0 +SER 21 -180.0 180.0 +D 22 -180.0 180.0 +nsup= 20 + nsup= 20 nstart_sup= 2 nstart_seq= 2 + NZ_START= 2 NZ_END= 21 + IZ_SC= 0 + Contact order: 0.308441558441558 + Shifting contacts: 2 2 + 1 ILE 5 ASN 2 + 2 TRP 7 TYR 4 + 3 LEU 8 TYR 4 + 4 LEU 8 ILE 5 + 5 LYS 9 GLN 6 + 6 GLY 12 TRP 7 + 7 GLY 12 LEU 8 + 8 SER 14 GLY 11 + 9 SER 15 ASP 10 + 10 SER 15 GLY 11 + 11 PRO 19 TRP 7 + 12 PRO 20 LEU 3 + 13 PRO 20 TYR 4 + 14 PRO 20 TRP 7 +Initial geometry will be read in. + +Geometry of the virtual chain. + Res d Theta Gamma Dsc Alpha Beta +D 1 0.000 0.000 0.000 0.000 0.000 0.000 +ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317 +LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685 +TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090 +ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666 +GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945 +TRP 7 3.800 84.466 51.434 2.605 152.178 38.024 +LEU 8 3.800 83.945 53.508 1.939 159.052 179.471 +LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090 +ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797 +GLY 11 3.800 94.602 67.604 0.000 0.000 0.000 +GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000 +PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163 +SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659 +SER 15 3.800 96.264 67.358 1.150 146.290 -130.305 +GLY 16 3.800 138.119 129.701 0.000 0.000 0.000 +ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747 +PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641 +PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044 +PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374 +SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303 +D 22 3.800 108.718 92.113 0.000 0.000 0.000 + + +******************************************************************************** + Processor 0: end reading molecular data. +******************************************************************************** + + +Energy evaluation or minimization calculation. + +Conformations will be energy-minimized. +******************************************************************************** + + Time for energy evaluation 0.000000000000000E+000 + +Virtual-chain energies: + +EVDW= -4.954316E+01 WEIGHT= 1.352790D+00 (SC-SC) +EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p) +EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p) +EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW) +ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching) +EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending) +ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local) +ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional) +ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional) +EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) +ECORR4= -8.338619E+01 WEIGHT= 4.288700D-01 (multi-body) +ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +EELLO= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local) +ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order) +ETURN4= -7.304754E+00 WEIGHT= 6.623000D-01 (turns, 4th order) +ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) +ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr) +EDIHC= 0.000000E+00 (dihedral angle constraints) +ESS= 0.000000E+00 (disulfide-bridge intrinsic energy) +UCONST= 0.000000E+00 (Constraint energy) +ETOT= -5.845169E+01 (total) +PP contact map: + 1 ASN 2 TYR 4 + 2 ASN 2 ILE 5 + 3 LEU 3 ILE 5 + 4 LEU 3 GLN 6 + 5 TYR 4 GLN 6 + 6 TYR 4 TRP 7 + 7 TYR 4 LEU 8 + 8 ILE 5 TRP 7 + 9 ILE 5 LEU 8 + 10 GLN 6 LEU 8 + 11 GLN 6 LYS 9 + 12 TRP 7 LYS 9 + 13 TRP 7 ASP 10 + 14 TRP 7 GLY 11 + 15 TRP 7 GLY 12 + 16 LEU 8 ASP 10 + 17 LEU 8 GLY 11 + 18 LYS 9 GLY 11 + 19 ASP 10 GLY 12 + 20 GLY 11 PRO 13 + 21 GLY 11 SER 14 + 22 GLY 12 SER 14 + 23 SER 14 GLY 16 + 24 SER 15 ARG 17 + 25 GLY 16 PRO 18 + 26 ARG 17 PRO 19 + 27 PRO 18 PRO 20 + Hairpins: +Constants of electrostatic interaction energy expression. + 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01 + 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01 + Total average electrostatic energy: -17.0351458449875 + VDW energy between peptide-group centers: -10.2064531653452 + + Electrostatic contacts before pruning: + 1 ASN 2 TYR 4 -1.06027 + 2 LEU 3 ILE 5 -1.59865 + 3 LEU 3 GLN 6 -0.54360 + 4 TYR 4 GLN 6 -2.10033 + 5 TYR 4 TRP 7 -0.84900 + 6 ILE 5 TRP 7 -1.85979 + 7 ILE 5 LEU 8 -0.53540 + 8 GLN 6 LEU 8 -1.48363 + 9 GLN 6 LYS 9 -0.61868 + 10 TRP 7 LYS 9 -1.55464 + 11 TRP 7 GLY 12 -0.37651 + 12 LEU 8 ASP 10 -0.61626 + 13 LEU 8 GLY 11 -0.40662 + + Electrostatic contacts after pruning: + 1 ASN 2 TYR 4 -1.06027 + 2 LEU 3 ILE 5 -1.59865 + 3 LEU 3 GLN 6 -0.54360 + 4 TYR 4 GLN 6 -2.10033 + 5 TYR 4 TRP 7 -0.84900 + 6 ILE 5 TRP 7 -1.85979 + 7 ILE 5 LEU 8 -0.53540 + 8 GLN 6 LEU 8 -1.48363 + 9 GLN 6 LYS 9 -0.61868 + 10 TRP 7 LYS 9 -1.55464 + 11 TRP 7 GLY 12 -0.37651 + 12 LEU 8 ASP 10 -0.61626 + 13 LEU 8 GLY 11 -0.40662 +Helix 1 2 10 + UNRES seq: + helix 3 11 + SC_move 1190 -36.8538206659302 +PP contact map: + 1 ASN 2 TYR 4 + 2 ASN 2 ILE 5 + 3 LEU 3 ILE 5 + 4 LEU 3 GLN 6 + 5 LEU 3 TRP 7 + 6 LEU 3 LEU 8 + 7 TYR 4 GLN 6 + 8 TYR 4 TRP 7 + 9 TYR 4 LEU 8 + 10 ILE 5 TRP 7 + 11 ILE 5 LEU 8 + 12 ILE 5 LYS 9 + 13 GLN 6 LEU 8 + 14 GLN 6 LYS 9 + 15 TRP 7 LYS 9 + 16 TRP 7 ASP 10 + 17 TRP 7 GLY 11 + 18 TRP 7 GLY 12 + 19 LEU 8 ASP 10 + 20 LEU 8 GLY 11 + 21 LEU 8 GLY 12 + 22 LYS 9 GLY 11 + 23 ASP 10 GLY 12 + 24 ASP 10 PRO 13 + 25 ASP 10 SER 14 + 26 GLY 11 PRO 13 + 27 GLY 11 SER 14 + 28 GLY 12 SER 14 + 29 PRO 13 SER 15 + 30 SER 14 GLY 16 + 31 SER 15 ARG 17 + 32 PRO 18 PRO 20 + Hairpins: +Constants of electrostatic interaction energy expression. + 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01 + 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01 + Total average electrostatic energy: -37.0692889481661 + VDW energy between peptide-group centers: 851.859545972044 + + Electrostatic contacts before pruning: + 1 ASN 2 TYR 4 -9.86113 + 2 ASN 2 ILE 5 -1.53124 + 3 LEU 3 ILE 5 -10.58267 + 4 LEU 3 GLN 6 -1.25110 + 5 LEU 3 TRP 7 -0.80052 + 6 TYR 4 GLN 6 -1.33813 + 7 TYR 4 TRP 7 -0.75936 + 8 ILE 5 TRP 7 -1.25974 + 9 ILE 5 LEU 8 -0.55583 + 10 GLN 6 LEU 8 -1.12670 + 11 GLN 6 LYS 9 -0.55504 + 12 TRP 7 LYS 9 -1.20931 + 13 TRP 7 GLY 12 -0.39500 + 14 LEU 8 ASP 10 -0.66375 + 15 LEU 8 GLY 11 -0.49451 + 16 ASP 10 SER 14 -0.49993 + 17 GLY 11 PRO 13 -0.96815 + + Electrostatic contacts after pruning: + 1 ASN 2 TYR 4 -9.86113 + 2 ASN 2 ILE 5 -1.53124 + 3 LEU 3 ILE 5 -10.58267 + 4 LEU 3 GLN 6 -1.25110 + 5 LEU 3 TRP 7 -0.80052 + 6 TYR 4 GLN 6 -1.33813 + 7 TYR 4 TRP 7 -0.75936 + 8 ILE 5 TRP 7 -1.25974 + 9 ILE 5 LEU 8 -0.55583 + 10 GLN 6 LEU 8 -1.12670 + 11 GLN 6 LYS 9 -0.55504 + 12 TRP 7 LYS 9 -1.20931 + 13 TRP 7 GLY 12 -0.39500 + 14 LEU 8 ASP 10 -0.66375 + 15 LEU 8 GLY 11 -0.49451 + 16 ASP 10 SER 14 -0.49993 + 17 GLY 11 PRO 13 -0.96815 +Helix 1 3 10 + UNRES seq: + helix 4 11 + +Virtual-chain energies: + +EVDW= 1.906975E+22 WEIGHT= 1.352790D+00 (SC-SC) +EVDW2= 2.099470E+04 WEIGHT= 1.593040D+00 (SC-p) +EES= -2.515997E+02 WEIGHT= 7.153400D-01 (p-p) +EVDWPP= 2.987216E+03 WEIGHT= 1.137100D-01 (p-p VDW) +ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching) +EBE= -9.194128E+00 WEIGHT= 1.138730D+00 (bending) +ESC= 5.035340E+32 WEIGHT= 1.625800D-01 (SC local) +ETORS= 8.926809E+00 WEIGHT= 1.985990D+00 (torsional) +ETORSD= -4.669374E-01 WEIGHT= 1.570690D+00 (double torsional) +EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) +ECORR4= -1.345056E+02 WEIGHT= 4.288700D-01 (multi-body) +ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +EELLO= NaN WEIGHT= 1.603600D-01 (electrostatic-local) +ETURN3= NaN WEIGHT= 1.687220D+00 (turns, 3rd order) +ETURN4= NaN WEIGHT= 6.623000D-01 (turns, 4th order) +ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) +ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr) +EDIHC= 0.000000E+00 (dihedral angle constraints) +ESS= 0.000000E+00 (disulfide-bridge intrinsic energy) +UCONST= 0.000000E+00 (Constraint energy) +ETOT= 1.000000E+99 (total) + +Geometry of the virtual chain. + Res d Theta Gamma Dsc Alpha Beta +D 1 0.000 0.000 0.000 0.000 0.000 0.000 +ASN 2 3.800 0.000 0.000 1.684 66.094 -81.746 +LEU 3 3.800 118.689 0.000 1.939 138.109 -26.893 +TYR 4 3.800 91.783 -149.590 2.484 123.984 108.154 +ILE 5 3.800 0.000 84.251 1.776 149.498 -90.988 +GLN 6 3.800 90.614 45.428 2.240 118.674 -118.972 +TRP 7 3.800 90.358 42.479 2.605 163.095 48.723 +LEU 8 3.800 90.561 45.576 1.939 145.280 -129.675 +LYS 9 3.800 90.389 50.728 2.541 133.176 -134.505 +ASP 10 3.800 91.852 44.664 1.709 133.932 -129.183 +GLY 11 3.800 90.570 70.394 0.000 180.000 180.000 +GLY 12 3.800 105.668 -67.487 0.000 180.000 180.000 +PRO 13 3.800 99.159 -65.573 1.345 115.572 -113.582 +SER 14 3.800 92.474 -33.144 1.150 113.504 -79.318 +SER 15 3.800 94.029 101.491 1.150 124.420 -158.647 +GLY 16 3.800 115.039 122.531 0.000 180.000 180.000 +ARG 17 3.800 94.980 -88.208 3.020 101.436 -102.179 +PRO 18 3.800 125.046 63.779 1.345 121.700 -130.547 +PRO 19 3.800 117.245 -83.662 1.345 110.939 -109.306 +PRO 20 3.800 121.153 -109.808 1.345 105.368 -111.814 +SER 21 3.800 92.281 -149.201 1.150 124.532 -120.711 +D 22 3.800 116.744 105.020 0.000 180.000 180.000 +RMS deviation from the reference structure: 2.344 + % of native contacts: 64.286 + % of nonnative contacts: 57.143 + contact order: 0.253 +SUMSL return code: 4 +# of energy evaluations: 553 +# of energy evaluations/sec: 3072.000 +CG processor 0 is finishing work. + Total wall clock time 0.242187500000000 sec diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.out_LJ000 b/examples/unres/MD/ff_gab/1L2Y_minim.out_LJ000 new file mode 100644 index 0000000..f1d12ca --- /dev/null +++ b/examples/unres/MD/ff_gab/1L2Y_minim.out_LJ000 @@ -0,0 +1,492 @@ +-------------------------------------------------------------------------------- + FILE ASSIGNMENT +-------------------------------------------------------------------------------- + Input file : 1L2Y_minim.inp + Output file : 1L2Y_minim.out_LJ000 + + Sidechain potential file : /users/adam/UNRES/PARAM/scinter_LJ.parm + SCp potential file : /users/adam/UNRES/PARAM/scp.parm + Electrostatic potential file : /users/adam/UNRES/PARAM/electr_631Gdp.parm + Cumulant coefficient file : + /users/adam/UNRES/PARAM/fourier_opt.parm.1igd_hc_iter3_3 + Torsional parameter file : /users/adam/UNRES/PARAM/torsion_631Gdp.parm + Double torsional parameter file : + /users/adam/UNRES/PARAM/torsion_double_631Gdp.parm + SCCOR parameter file : /users/adam/UNRES/PARAM/rotcorr_AM1.parm + Bond & inertia constant file : /users/adam/UNRES/PARAM/bond.parm + Bending parameter file : /users/adam/UNRES/PARAM/thetaml.5parm + Rotamer parameter file : /users/adam/UNRES/PARAM/scgauss.parm + Threading database : /users/adam/UNRES/PARAM/patterns.cart +-------------------------------------------------------------------------------- +******************************************************************************** +United-residue force field calculation - parallel job. +******************************************************************************** + ### LAST MODIFIED 03/28/12 23:29 by czarek + ++++ Compile info ++++ + Version 2.5 build 62 + compiled Sun May 13 16:07:22 2012 + compiled by adam@matrix.chem.cornell.edu + OS name: Linux + OS release: 2.6.34.9-69.fc13.x86_64 + OS version: #1 SMP Tue May 3 09:23:03 UTC 2011 + flags: + INSTALL_DIR = /users/software/mpich-1.2.7p1_int... + FC= ifort + OPT = -O3 -ip -w + FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include + FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)... + FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include + FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ... + LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr... + ARCH = LINUX + PP = /lib/cpp -P + object = unres.o arcos.o cartprint.o chainbuild... + GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ... + GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP... + E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR... + E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort... + ++++ End of compile info ++++ + +Potential is LJ , exponents are 6 12 + +Disulfide bridge parameters: +S-S bridge energy: -5.50 +d0cm: 3.78 akcm: 15.10 +akth: 11.00 akct: 12.00 +v1ss: -1.08 v2ss: 7.61 v3ss: 13.70 + MPI: node= 0 iseed(4)= 0 0 -46 + -45086 + ran_num 6.422640197456531E-013 +RMSDBC = 3.0 +RMSDBC1 = 0.5 +RMSDBC1MAX = 1.5 +DRMS = 0.1 +RMSDBCM = 3.0 +Time limit (min): 960.0 + RESCALE_MODE 1 +Library routine used to diagonalize matrices. + +******************************************************************************** + Options in energy minimization: +******************************************************************************** +MaxMin: 2000 MaxFun: 5000MinMin: 2000 MinFun: 2000 TolF: 1.00000E-02 RTolF: 1.00000E-04 + +Energy-term weights (unscaled): + +WSCC= 1.352790 (SC-SC) +WSCP= 1.593040 (SC-p) +WELEC= 0.715340 (p-p electr) +WVDWPP= 0.113710 (p-p VDW) +WBOND= 1.000000 (stretching) +WANG= 1.138730 (bending) +WSCLOC= 0.162580 (SC local) +WTOR= 1.985990 (torsional) +WTORD= 1.570690 (double torsional) +WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) +WEL_LOC= 0.160360 (multi-body 3-rd order) +WCORR4= 0.428870 (multi-body 4th order) +WCORR5= 0.000000 (multi-body 5th order) +WCORR6= 0.000000 (multi-body 6th order) +WSCCOR= 0.000000 (back-scloc correlation) +WTURN3= 1.687220 (turns, 3rd order) +WTURN4= 0.662300 (turns, 4th order) +WTURN6= 0.000000 (turns, 6th order) + +Hydrogen-bonding correlation between contact pairs of peptide groups + +Scaling factor of 1,4 SC-p interactions: 0.400 +General scaling factor of SC-p interactions: 1.000 + +Energy-term weights (scaled): + +WSCC= 1.352790 (SC-SC) +WSCP= 1.593040 (SC-p) +WELEC= 0.715340 (p-p electr) +WVDWPP= 0.113710 (p-p VDW) +WBOND= 1.000000 (stretching) +WANG= 1.138730 (bending) +WSCLOC= 0.162580 (SC local) +WTOR= 1.985990 (torsional) +WTORD= 1.570690 (double torsional) +WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) +WEL_LOC= 0.160360 (multi-body 3-rd order) +WCORR4= 0.428870 (multi-body 4th order) +WCORR5= 0.000000 (multi-body 5th order) +WCORR6= 0.000000 (multi-body 6th order) +WSCCOR= 0.000000 (back-scloc correlatkion) +WTURN3= 1.687220 (turns, 3rd order) +WTURN4= 0.662300 (turns, 4th order) +WTURN6= 0.000000 (turns, 6th order) + Reference temperature for weights calculation: 300.000000000000 + Parameters of the SS-bond potential: + D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH + 11.0000000000000 AKCT 12.0000000000000 + V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS + 13.7000000000000 + EBR -5.50000000000000 +PDB data will be read from file 1L2Y.pdb + Nres: 21 +Backbone and SC coordinates as read from the PDB + 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051 + 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437 + 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850 + 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797 + 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074 + 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853 + 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450 + 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799 + 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146 + 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676 + 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593 + 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723 + 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058 + 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675 + 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546 + 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870 + 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986 + 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688 + 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856 + 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430 + 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488 + 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754 +nsup= 20 nstart_sup= 2 + ITEL + 1 21 0 + 2 14 1 + 3 5 1 + 4 8 1 + 5 4 1 + 6 13 1 + 7 7 1 + 8 5 1 + 9 19 1 + 10 16 1 + 11 10 1 + 12 10 2 + 13 20 1 + 14 12 1 + 15 12 1 + 16 10 1 + 17 18 2 + 18 20 2 + 19 20 2 + 20 20 1 + 21 12 0 + ns= 0 iss: +Boundaries in phi angle sampling: +D 1 -180.0 180.0 +ASN 2 -180.0 180.0 +LEU 3 -180.0 180.0 +TYR 4 -180.0 180.0 +ILE 5 -180.0 180.0 +GLN 6 -180.0 180.0 +TRP 7 -180.0 180.0 +LEU 8 -180.0 180.0 +LYS 9 -180.0 180.0 +ASP 10 -180.0 180.0 +GLY 11 -180.0 180.0 +GLY 12 -180.0 180.0 +PRO 13 -180.0 180.0 +SER 14 -180.0 180.0 +SER 15 -180.0 180.0 +GLY 16 -180.0 180.0 +ARG 17 -180.0 180.0 +PRO 18 -180.0 180.0 +PRO 19 -180.0 180.0 +PRO 20 -180.0 180.0 +SER 21 -180.0 180.0 +D 22 -180.0 180.0 +nsup= 20 + nsup= 20 nstart_sup= 2 nstart_seq= 2 + NZ_START= 2 NZ_END= 21 + IZ_SC= 0 + Contact order: 0.320158102766798 + Shifting contacts: 2 2 + 1 ILE 5 ASN 2 + 2 TRP 7 TYR 4 + 3 LEU 8 TYR 4 + 4 LEU 8 ILE 5 + 5 LYS 9 GLN 6 + 6 GLY 11 TRP 7 + 7 GLY 11 LEU 8 + 8 GLY 12 TRP 7 + 9 GLY 12 LEU 8 + 10 PRO 13 TRP 7 + 11 SER 14 GLY 11 + 12 SER 15 TRP 7 + 13 SER 15 ASP 10 + 14 SER 15 GLY 11 + 15 SER 15 GLY 12 + 16 ARG 17 TRP 7 + 17 ARG 17 ASP 10 + 18 PRO 18 TRP 7 + 19 PRO 19 TYR 4 + 20 PRO 19 TRP 7 + 21 PRO 20 LEU 3 + 22 PRO 20 TYR 4 + 23 PRO 20 TRP 7 +Initial geometry will be read in. + +Geometry of the virtual chain. + Res d Theta Gamma Dsc Alpha Beta +D 1 0.000 0.000 0.000 0.000 0.000 0.000 +ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317 +LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685 +TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090 +ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666 +GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945 +TRP 7 3.800 84.466 51.434 2.605 152.178 38.024 +LEU 8 3.800 83.945 53.508 1.939 159.052 179.471 +LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090 +ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797 +GLY 11 3.800 94.602 67.604 0.000 0.000 0.000 +GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000 +PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163 +SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659 +SER 15 3.800 96.264 67.358 1.150 146.290 -130.305 +GLY 16 3.800 138.119 129.701 0.000 0.000 0.000 +ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747 +PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641 +PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044 +PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374 +SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303 +D 22 3.800 108.718 92.113 0.000 0.000 0.000 + + +******************************************************************************** + Processor 0: end reading molecular data. +******************************************************************************** + + +Energy evaluation or minimization calculation. + +Conformations will be energy-minimized. +******************************************************************************** + + Time for energy evaluation 0.000000000000000E+000 + +Virtual-chain energies: + +EVDW= 6.950763E+00 WEIGHT= 1.352790D+00 (SC-SC) +EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p) +EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p) +EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW) +ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching) +EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending) +ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local) +ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional) +ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional) +EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) +ECORR4= -8.338619E+01 WEIGHT= 4.288700D-01 (multi-body) +ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +EELLO= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local) +ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order) +ETURN4= -7.304754E+00 WEIGHT= 6.623000D-01 (turns, 4th order) +ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) +ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr) +EDIHC= 0.000000E+00 (dihedral angle constraints) +ESS= 0.000000E+00 (disulfide-bridge intrinsic energy) +UCONST= 0.000000E+00 (Constraint energy) +ETOT= 1.797273E+01 (total) +PP contact map: + 1 ASN 2 TYR 4 + 2 ASN 2 ILE 5 + 3 LEU 3 ILE 5 + 4 LEU 3 GLN 6 + 5 TYR 4 GLN 6 + 6 TYR 4 TRP 7 + 7 TYR 4 LEU 8 + 8 ILE 5 TRP 7 + 9 ILE 5 LEU 8 + 10 GLN 6 LEU 8 + 11 GLN 6 LYS 9 + 12 TRP 7 LYS 9 + 13 TRP 7 ASP 10 + 14 TRP 7 GLY 11 + 15 TRP 7 GLY 12 + 16 LEU 8 ASP 10 + 17 LEU 8 GLY 11 + 18 LYS 9 GLY 11 + 19 ASP 10 GLY 12 + 20 GLY 11 PRO 13 + 21 GLY 11 SER 14 + 22 GLY 12 SER 14 + 23 SER 14 GLY 16 + 24 SER 15 ARG 17 + 25 GLY 16 PRO 18 + 26 ARG 17 PRO 19 + 27 PRO 18 PRO 20 + Hairpins: +Constants of electrostatic interaction energy expression. + 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01 + 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01 + Total average electrostatic energy: -17.0351458449875 + VDW energy between peptide-group centers: -10.2064531653452 + + Electrostatic contacts before pruning: + 1 ASN 2 TYR 4 -1.06027 + 2 LEU 3 ILE 5 -1.59865 + 3 LEU 3 GLN 6 -0.54360 + 4 TYR 4 GLN 6 -2.10033 + 5 TYR 4 TRP 7 -0.84900 + 6 ILE 5 TRP 7 -1.85979 + 7 ILE 5 LEU 8 -0.53540 + 8 GLN 6 LEU 8 -1.48363 + 9 GLN 6 LYS 9 -0.61868 + 10 TRP 7 LYS 9 -1.55464 + 11 TRP 7 GLY 12 -0.37651 + 12 LEU 8 ASP 10 -0.61626 + 13 LEU 8 GLY 11 -0.40662 + + Electrostatic contacts after pruning: + 1 ASN 2 TYR 4 -1.06027 + 2 LEU 3 ILE 5 -1.59865 + 3 LEU 3 GLN 6 -0.54360 + 4 TYR 4 GLN 6 -2.10033 + 5 TYR 4 TRP 7 -0.84900 + 6 ILE 5 TRP 7 -1.85979 + 7 ILE 5 LEU 8 -0.53540 + 8 GLN 6 LEU 8 -1.48363 + 9 GLN 6 LYS 9 -0.61868 + 10 TRP 7 LYS 9 -1.55464 + 11 TRP 7 GLY 12 -0.37651 + 12 LEU 8 ASP 10 -0.61626 + 13 LEU 8 GLY 11 -0.40662 +Helix 1 2 10 + UNRES seq: + helix 3 11 + SC_move 1189 -4.13326717681629 +PP contact map: + 1 ASN 2 TYR 4 + 2 ASN 2 ILE 5 + 3 LEU 3 ILE 5 + 4 LEU 3 GLN 6 + 5 LEU 3 TRP 7 + 6 TYR 4 GLN 6 + 7 TYR 4 TRP 7 + 8 ILE 5 TRP 7 + 9 ILE 5 LEU 8 + 10 GLN 6 LEU 8 + 11 GLN 6 LYS 9 + 12 TRP 7 LYS 9 + 13 TRP 7 ASP 10 + 14 TRP 7 GLY 11 + 15 TRP 7 GLY 12 + 16 LEU 8 ASP 10 + 17 LEU 8 GLY 11 + 18 LYS 9 GLY 11 + 19 ASP 10 GLY 12 + 20 GLY 11 PRO 13 + 21 GLY 11 SER 14 + 22 GLY 12 SER 14 + 23 PRO 13 SER 15 + 24 PRO 13 PRO 18 + 25 SER 14 GLY 16 + 26 SER 14 ARG 17 + 27 SER 15 ARG 17 + 28 PRO 18 PRO 20 + Hairpins: +Constants of electrostatic interaction energy expression. + 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01 + 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 + 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01 + Total average electrostatic energy: -34.0939296423320 + VDW energy between peptide-group centers: 899.113237730561 + + Electrostatic contacts before pruning: + 1 ASN 2 TYR 4 -10.17518 + 2 ASN 2 ILE 5 -1.20257 + 3 LEU 3 ILE 5 -10.90405 + 4 LEU 3 GLN 6 -1.04733 + 5 LEU 3 TRP 7 -0.51328 + 6 TYR 4 GLN 6 -1.11943 + 7 TYR 4 TRP 7 -0.47363 + 8 ILE 5 TRP 7 -1.27116 + 9 GLN 6 LEU 8 -0.57639 + 10 TRP 7 LYS 9 -1.27183 + 11 TRP 7 ASP 10 -0.33671 + 12 LEU 8 ASP 10 -0.74960 + 13 LEU 8 GLY 11 -0.44794 + 14 GLY 12 SER 14 -0.51788 + + Electrostatic contacts after pruning: + 1 ASN 2 TYR 4 -10.17518 + 2 ASN 2 ILE 5 -1.20257 + 3 LEU 3 ILE 5 -10.90405 + 4 LEU 3 GLN 6 -1.04733 + 5 LEU 3 TRP 7 -0.51328 + 6 TYR 4 GLN 6 -1.11943 + 7 TYR 4 TRP 7 -0.47363 + 8 ILE 5 TRP 7 -1.27116 + 9 GLN 6 LEU 8 -0.57639 + 10 TRP 7 LYS 9 -1.27183 + 11 TRP 7 ASP 10 -0.33671 + 12 LEU 8 ASP 10 -0.74960 + 13 LEU 8 GLY 11 -0.44794 + 14 GLY 12 SER 14 -0.51788 +Helix 1 1 7 + UNRES seq: + helix 2 8 + +Virtual-chain energies: + +EVDW= 6.783553E+02 WEIGHT= 1.352790D+00 (SC-SC) +EVDW2= 2.098526E+04 WEIGHT= 1.593040D+00 (SC-p) +EES= -2.316959E+02 WEIGHT= 7.153400D-01 (p-p) +EVDWPP= 3.102288E+03 WEIGHT= 1.137100D-01 (p-p VDW) +ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching) +EBE= -1.030472E+01 WEIGHT= 1.138730D+00 (bending) +ESC= 5.035340E+32 WEIGHT= 1.625800D-01 (SC local) +ETORS= 8.256991E+00 WEIGHT= 1.985990D+00 (torsional) +ETORSD= 1.541091E+00 WEIGHT= 1.570690D+00 (double torsional) +EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) +ECORR4= -1.142431E+02 WEIGHT= 4.288700D-01 (multi-body) +ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +EELLO= NaN WEIGHT= 1.603600D-01 (electrostatic-local) +ETURN3= NaN WEIGHT= 1.687220D+00 (turns, 3rd order) +ETURN4= NaN WEIGHT= 6.623000D-01 (turns, 4th order) +ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) +ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr) +EDIHC= 0.000000E+00 (dihedral angle constraints) +ESS= 0.000000E+00 (disulfide-bridge intrinsic energy) +UCONST= 0.000000E+00 (Constraint energy) +ETOT= 1.000000E+99 (total) + +Geometry of the virtual chain. + Res d Theta Gamma Dsc Alpha Beta +D 1 0.000 0.000 0.000 0.000 0.000 0.000 +ASN 2 3.800 0.000 0.000 1.684 166.403 -78.295 +LEU 3 3.800 118.535 0.000 1.939 98.410 -20.526 +TYR 4 3.800 91.262 -84.783 2.484 143.962 -14.485 +ILE 5 3.800 0.000 74.731 1.776 126.981 -107.717 +GLN 6 3.800 90.125 49.156 2.240 123.165 -131.319 +TRP 7 3.800 89.563 53.467 2.605 136.415 -30.509 +LEU 8 3.800 89.157 49.735 1.939 155.047 -119.048 +LYS 9 3.800 90.266 80.355 2.541 138.316 -137.964 +ASP 10 3.800 91.711 42.732 1.709 143.742 -133.222 +GLY 11 3.800 91.876 63.556 0.000 180.000 180.000 +GLY 12 3.800 115.894 -57.622 0.000 180.000 180.000 +PRO 13 3.800 120.076 -75.407 1.345 106.478 -96.392 +SER 14 3.800 92.479 -68.391 1.150 133.923 -99.369 +SER 15 3.800 94.169 65.963 1.150 114.383 -74.889 +GLY 16 3.800 93.692 138.023 0.000 180.000 180.000 +ARG 17 3.800 94.409 -73.682 3.020 95.051 -65.680 +PRO 18 3.800 130.488 58.633 1.345 120.711 -129.430 +PRO 19 3.800 117.860 -103.495 1.345 125.023 -135.544 +PRO 20 3.800 116.631 -108.533 1.345 97.647 -118.910 +SER 21 3.800 93.213 -137.715 1.150 119.341 -84.219 +D 22 3.800 120.091 73.011 0.000 180.000 180.000 +RMS deviation from the reference structure: 2.378 + % of native contacts: 60.870 + % of nonnative contacts: 39.130 + contact order: 0.300 +SUMSL return code: 4 +# of energy evaluations: 431 +# of energy evaluations/sec: 3335.758 +CG processor 0 is finishing work. + Total wall clock time 0.195312500000000 sec diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB.int b/examples/unres/MD/ff_gab/1L2Y_minim_GB.int new file mode 100644 index 0000000..2f9bf8c --- /dev/null +++ b/examples/unres/MD/ff_gab/1L2Y_minim_GB.int @@ -0,0 +1,13 @@ + 0 -78.629 0 + 118.4938 91.7167 90.0355 89.0402 90.4331 90.7695 90.5004 92.1025 + 91.3597 111.6806 113.6844 93.2625 93.9321 115.8645 94.3034 121.7562 + 117.8557 115.6233 93.8548 117.7927 + -100.4277 63.6464 55.7934 45.2757 45.2407 50.3196 46.2887 65.7510 + -71.6699 -58.6548 -78.1521 57.8486 137.4148 -84.3592 61.6350 -81.0853 + -108.3267 -137.4501 46.0495 + 110.7016 141.2278 118.5494 146.6522 104.8935 138.7112 136.3949 134.1788 + 143.4752 180.0000 180.0000 129.7747 115.0099 124.8976 180.0000 90.1761 + 116.3394 141.9872 97.8769 144.1295 + -85.6852 -49.5399 113.8683 -96.9727 -50.5662 59.2188 -145.4804 -136.3182 + -124.4460 180.0000 180.0000 -154.0107 -77.0566 -144.2941 180.0000 -107.6874 + -177.3783 -158.7148 -97.6530 -129.5456 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB.mol2 b/examples/unres/MD/ff_gab/1L2Y_minim_GB.mol2 new file mode 100644 index 0000000..e69de29 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB.pdb b/examples/unres/MD/ff_gab/1L2Y_minim_GB.pdb new file mode 100644 index 0000000..e69de29 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB.stat b/examples/unres/MD/ff_gab/1L2Y_minim_GB.stat new file mode 100644 index 0000000..e69de29 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB000.int b/examples/unres/MD/ff_gab/1L2Y_minim_GB000.int new file mode 100644 index 0000000..e64ba47 --- /dev/null +++ b/examples/unres/MD/ff_gab/1L2Y_minim_GB000.int @@ -0,0 +1,13 @@ + 0************ 0 + 118.6889 91.7826 0.0000 90.6142 90.3584 90.5610 90.3893 91.8517 + 90.5697 105.6675 99.1585 92.4742 94.0291 115.0390 94.9803 125.0459 + 117.2452 121.1533 92.2810 116.7440 + -149.5898 84.2508 45.4276 42.4792 45.5761 50.7277 44.6644 70.3941 + -67.4870 -65.5727 -33.1437 101.4914 122.5310 -88.2079 63.7788 -83.6619 + -109.8078 -149.2012 105.0201 + 66.0940 138.1088 123.9842 149.4976 118.6739 163.0952 145.2796 133.1762 + 133.9319 180.0000 180.0000 115.5719 113.5038 124.4199 180.0000 101.4361 + 121.6996 110.9385 105.3684 124.5323 + -81.7460 -26.8931 108.1542 -90.9882 -118.9725 48.7228 -129.6748 -134.5051 + -129.1828 180.0000 180.0000 -113.5817 -79.3178 -158.6472 180.0000 -102.1785 + -130.5467 -109.3060 -111.8144 -120.7112 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB000.mol2 b/examples/unres/MD/ff_gab/1L2Y_minim_GB000.mol2 new file mode 100644 index 0000000..e69de29 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB000.pdb b/examples/unres/MD/ff_gab/1L2Y_minim_GB000.pdb new file mode 100644 index 0000000..e69de29 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB000.stat b/examples/unres/MD/ff_gab/1L2Y_minim_GB000.stat new file mode 100644 index 0000000..e69de29 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.int b/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.int new file mode 100644 index 0000000..707ee24 --- /dev/null +++ b/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.int @@ -0,0 +1,13 @@ + 0************ 0 + 118.5349 91.2615 0.0000 90.1249 89.5628 89.1570 90.2660 91.7107 + 91.8763 115.8941 120.0758 92.4795 94.1689 93.6918 94.4088 130.4883 + 117.8596 116.6312 93.2127 120.0906 + -84.7829 74.7307 49.1557 53.4670 49.7352 80.3551 42.7322 63.5565 + -57.6216 -75.4075 -68.3913 65.9628 138.0231 -73.6821 58.6330 -103.4954 + -108.5326 -137.7154 73.0113 + 166.4029 98.4096 143.9619 126.9814 123.1648 136.4149 155.0468 138.3159 + 143.7423 180.0000 180.0000 106.4783 133.9230 114.3826 180.0000 95.0507 + 120.7111 125.0235 97.6472 119.3410 + -78.2954 -20.5265 -14.4853 -107.7166 -131.3195 -30.5095 -119.0482 -137.9641 + -133.2218 180.0000 180.0000 -96.3923 -99.3690 -74.8894 180.0000 -65.6796 + -129.4301 -135.5437 -118.9101 -84.2187 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.mol2 b/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.mol2 new file mode 100644 index 0000000..e69de29 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.pdb b/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.pdb new file mode 100644 index 0000000..e69de29 diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.stat b/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.stat new file mode 100644 index 0000000..e69de29 diff --git a/examples/unres/MD/ff_gab/fort.12 b/examples/unres/MD/ff_gab/fort.12 new file mode 100644 index 0000000..817ff02 --- /dev/null +++ b/examples/unres/MD/ff_gab/fort.12 @@ -0,0 +1,8 @@ +DefPropRes 'helix1' 'num = 2.. 9' +DefPropRes 'helix' 'helix1' +DefPropRes 'coil' '! (helix | sheet)' +XMacStand ribbon.mac +DefPropRes 'helix1' 'num = 3.. 9' +DefPropRes 'helix' 'helix1' +DefPropRes 'coil' '! (helix | sheet)' +XMacStand ribbon.mac diff --git a/examples/unres/MD/ff_gab/start.mat b/examples/unres/MD/ff_gab/start.mat new file mode 100755 index 0000000..a1008ff --- /dev/null +++ b/examples/unres/MD/ff_gab/start.mat @@ -0,0 +1,12 @@ +#PBS -N test +#PBS -q dque +#PBS -l nodes=1:ppn=1 +#PBS -l mem=2gb +#PBS -l walltime=24:00:00 + +setenv MPIRUN "/users/software/mpich-1.2.7p1_intel-10.1_em64_ssh/bin/mpirun " +setenv NPROCS `cat $PBS_NODEFILE | wc -l` + +cd $PBS_O_WORKDIR +$MPIRUN -machinefile $PBS_NODEFILE -np $NPROCS ./unres.csh + diff --git a/examples/unres/MD/ff_gab/test.e54333 b/examples/unres/MD/ff_gab/test.e54333 new file mode 100644 index 0000000..0a57c6d --- /dev/null +++ b/examples/unres/MD/ff_gab/test.e54333 @@ -0,0 +1 @@ +Bye Bye... diff --git a/examples/unres/MD/ff_gab/test.e54334 b/examples/unres/MD/ff_gab/test.e54334 new file mode 100644 index 0000000..0a57c6d --- /dev/null +++ b/examples/unres/MD/ff_gab/test.e54334 @@ -0,0 +1 @@ +Bye Bye... diff --git a/examples/unres/MD/ff_gab/test.o54333 b/examples/unres/MD/ff_gab/test.o54333 new file mode 100644 index 0000000..4a70449 --- /dev/null +++ b/examples/unres/MD/ff_gab/test.o54333 @@ -0,0 +1,23 @@ + Processor 0 out of 1 rank in CG_COMM 0 + size of CG_COMM 1 size of FG_COMM 1 rank in FG_COMM1 + 0 size of FG_COMM1 1 +Inside initialize MPI: node= 0 iseed(4)= 0 0 -46 + -45086 + indpdb= 0 pdbref= T + Call Read_Bridge. + ns= 0 + Processor 0 0 0 ivec_start 1 ivec_end + 21 + after etotal + Calling OVERLAP_SC + SC_move 1189 -4.13326717681629 + Calling MINIMIZE. + SUMSL return code is 4 eval 430 + # eval/s 3335.75757575758 + refstr= T +CG processor 0 is finishing work. +-------------------------------------- +Running PBS epilogue script + +Single processor job or ~/.nokill exist, no need to kill processes +Done. diff --git a/examples/unres/MD/ff_gab/test.o54334 b/examples/unres/MD/ff_gab/test.o54334 new file mode 100644 index 0000000..40667c9 --- /dev/null +++ b/examples/unres/MD/ff_gab/test.o54334 @@ -0,0 +1,23 @@ + Processor 0 out of 1 rank in CG_COMM 0 + size of CG_COMM 1 size of FG_COMM 1 rank in FG_COMM1 + 0 size of FG_COMM1 1 +Inside initialize MPI: node= 0 iseed(4)= 0 0 -46 + -45086 + indpdb= 0 pdbref= T + Call Read_Bridge. + ns= 0 + Processor 0 0 0 ivec_start 1 ivec_end + 21 + after etotal + Calling OVERLAP_SC + SC_move 1190 -36.8538206659302 + Calling MINIMIZE. + SUMSL return code is 4 eval 552 + # eval/s 3072.00000000000 + refstr= T +CG processor 0 is finishing work. +-------------------------------------- +Running PBS epilogue script + +Single processor job or ~/.nokill exist, no need to kill processes +Done. diff --git a/examples/unres/MD/ff_gab/unres.csh b/examples/unres/MD/ff_gab/unres.csh new file mode 100755 index 0000000..82b2f43 --- /dev/null +++ b/examples/unres/MD/ff_gab/unres.csh @@ -0,0 +1,31 @@ +#!/bin/csh -f +# Script to run the program unresCSA on linux with MPICH/PBS (parallel version). +# + +setenv OUT1FILE YES +setenv FGPROCS 1 +setenv POT GB +setenv PREFIX 1L2Y_minim + +set DD = /users/adam/UNRES/PARAM +setenv UNRES_BIN /users/adam/unres/bin/unres/MD/unres_ifort_MPICH_GAB.exe +#setenv UNRES_BIN /users/adam/unres/bin/unres/MD/unres_ifort_single_GAB.exe +#--------------------------------- +setenv BONDPAR $DD/bond.parm +setenv THETPAR $DD/thetaml.5parm +setenv ROTPAR $DD/scgauss.parm +setenv TORPAR $DD/torsion_631Gdp.parm +setenv TORDPAR $DD/torsion_double_631Gdp.parm +setenv ELEPAR $DD/electr_631Gdp.parm +setenv SIDEPAR ${DD}/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k +#setenv SIDEPAR ${DD}/scinter_LJ.parm +setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3 +setenv SCPPAR $DD/scp.parm +setenv SCCORPAR $DD/rotcorr_AM1.parm + +# Pattern database +setenv PATTERN $DD/patterns.cart +#-------------------------------------------- + +$UNRES_BIN $* + diff --git a/examples/unres/MD/ff_gab/unres_single.sh b/examples/unres/MD/ff_gab/unres_single.sh index 49c2cc2..0576f87 100755 --- a/examples/unres/MD/ff_gab/unres_single.sh +++ b/examples/unres/MD/ff_gab/unres_single.sh @@ -2,9 +2,9 @@ export POT=$1 export PREFIX=$2 #----------------------------------------------------------------------------- -UNRES_BIN=../../../../bin/unres/MD/unres_gfortran_single.exe +UNRES_BIN=../../../../bin/unres/MD/unres_ifort_single_GAB.exe #----------------------------------------------------------------------------- -DD=../../PARAM +DD=../../../../PARAM export BONDPAR=$DD/bond.parm export THETPAR=$DD/thetaml.5parm export ROTPAR=$DD/scgauss.parm @@ -14,6 +14,7 @@ export ELEPAR=$DD/electr_631Gdp.parm export SIDEPAR=$DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k export FOURIER=$DD/fourier_opt.parm.1igd_hc_iter3_3 export SCPPAR=$DD/scp.parm +export SCCORPAR=$DD/rotcorr_AM1.parm export PATTERN=$DD/patterns.cart #----------------------------------------------------------------------------- $UNRES_BIN diff --git a/source/wham/src/cinfo.f b/source/wham/src/cinfo.f index 5ecce7a..97eabbe 100644 --- a/source/wham/src/cinfo.f +++ b/source/wham/src/cinfo.f @@ -1,10 +1,10 @@ C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C -C 0 0 546 +C 0 0 565 subroutine cinfo include 'COMMON.IOUNITS' write(iout,*)'++++ Compile info ++++' - write(iout,*)'Version 0.0 build 546' - write(iout,*)'compiled Sun May 20 07:28:19 2012' + write(iout,*)'Version 0.0 build 565' + write(iout,*)'compiled Tue May 29 04:48:26 2012' write(iout,*)'compiled by adam@matrix.chem.cornell.edu' write(iout,*)'OS name: Linux ' write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 ' diff --git a/source/wham/src/wham_calc1.F b/source/wham/src/wham_calc1.F index 5783bd4..a6044cd 100644 --- a/source/wham/src/wham_calc1.F +++ b/source/wham/src/wham_calc1.F @@ -38,6 +38,7 @@ c parameter (MaxHdim=200000) parameter (MaxPoint=MaxStr, & MaxPointProc=MaxStr_Proc) double precision finorm_max,potfac,entmin,entmax,expfac,vf + double precision entfac_min,entfac_min_t parameter (finorm_max=1.0d0) integer islice integer i,ii,j,jj,k,kk,l,m,ind,iter,t,tmax,ient,ientmax,iln @@ -48,7 +49,8 @@ c parameter (MaxHdim=200000) double precision energia(0:max_ene) #ifdef MPI integer tmax_t,upindE_p - double precision fi_p(MaxR,MaxT_h,Max_Parm) + double precision fi_p(MaxR,MaxT_h,Max_Parm), + & fi_p_min(MaxR,MaxT_h,Max_Parm) double precision sumW_p(0:Max_GridT,Max_Parm), & sumE_p(0:Max_GridT,Max_Parm),sumEsq_p(0:Max_GridT,Max_Parm), & sumQ_p(MaxQ1,0:Max_GridT,Max_Parm), @@ -71,6 +73,7 @@ c parameter (MaxHdim=200000) & sumEprim(0:NGridT,Max_Parm),sumEbis(0:NGridT,Max_Parm),betaT, & weight,econstr double precision fi(MaxR,maxT_h,Max_Parm), + & fi_min(MaxR,maxT_h,Max_Parm), & dd,dd1,dd2,hh,dmin,denom,finorm,avefi,pom, & hfin(0:MaxHdim,maxT_h),histE(0:maxindE), & hrmsrgy(0:MaxBinRgy,0:MaxBinRms,maxT_h), @@ -368,6 +371,7 @@ c write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft ! Compute new free-energy values corresponding to the righ-hand side of the ! equation and their derivatives. write (iout,*) "------------------------fi" + entfac_min=1.0d10 #ifdef MPI do t=1,scount(me1) #else @@ -393,10 +397,67 @@ c write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft enddo enddo entfac(t)=-dlog(denom)-vmax + if (entfac(t).lt.entfac_min) entfac_min=entfac(t) #ifdef DEBUG write (iout,*) t,"vmax",vmax," denom",denom,"entfac",entfac(t) #endif enddo +c#ifdef MPI +c write (iout,*) "entfac_min before AllReduce",entfac_min +c call MPI_AllReduce(entfac_min,entfac_min_t,1, +c & MPI_DOUBLE_PRECISION,MPI_MAX,WHAM_COMM,IERROR) +c entfac_min=entfac_min_t +c write (iout,*) "entfac_min after AllReduce",entfac_min +c#endif +c#ifdef MPI +c do t=1,scount(me) +c entfac(t)=entfac(t)-entfac_min +c enddo +c#else +c do t=1,ntot(islice) +c entfac(t)=entfac(t)-entfac_min +c enddo +c#endif + do iparm=1,nParmSet + do iib=1,nT_h(iparm) + do ii=1,nR(iib,iparm) +#ifdef MPI + fi_p_min(ii,iib,iparm)=-1.0d10 + do t=1,scount(me) + aux=v(t,ii,iib,iparm)+entfac(t) + if (aux.gt.fi_p_min(ii,iib,iparm)) + & fi_p_min(ii,iib,iparm)=aux + enddo +#else + do t=1,ntot(islice) + aux=v(t,ii,iib,iparm)+entfac(t) + if (aux.gt.fi_min(ii,iib,iparm)) + & fi_min(ii,iib,iparm)=aux + enddo +#endif + enddo ! ii + enddo ! iib + enddo ! iparm +#ifdef MPI +#ifdef DEBUG + write (iout,*) "fi_min before AllReduce" + do i=1,nParmSet + do j=1,nT_h(i) + write (iout,*) (i,j,k,fi_p_min(k,j,i),k=1,nR(j,i)) + enddo + enddo +#endif + call MPI_AllReduce(fi_p_min,fi_min,MaxR*MaxT_h*nParmSet, + & MPI_DOUBLE_PRECISION,MPI_MAX,WHAM_COMM,IERROR) +#ifdef DEBUG + write (iout,*) "fi_min after AllReduce" + do i=1,nParmSet + do j=1,nT_h(i) + write (iout,*) (i,j,k,fi_min(k,j,i),k=1,nR(j,i)) + enddo + enddo +#endif +#endif do iparm=1,nParmSet do iib=1,nT_h(iparm) do ii=1,nR(iib,iparm) @@ -404,17 +465,18 @@ c write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft fi_p(ii,iib,iparm)=0.0d0 do t=1,scount(me) fi_p(ii,iib,iparm)=fi_p(ii,iib,iparm) - & +dexp(v(t,ii,iib,iparm)+entfac(t)) + & +dexp(v(t,ii,iib,iparm)+entfac(t)-fi_min(ii,iib,iparm)) #ifdef DEBUG - write (iout,'(4i5,3e15.5)') t,ii,iib,iparm, - & v(t,ii,iib,iparm),entfac(t),fi_p(ii,iib,iparm) + write (iout,'(4i5,4e15.5)') t,ii,iib,iparm, + & v(t,ii,iib,iparm),entfac(t),fi_min(ii,iib,iparm), + & fi_p(ii,iib,iparm) #endif enddo #else fi(ii,iib,iparm)=0.0d0 do t=1,ntot(islice) fi(ii,iib,iparm)=fi(ii,iib,iparm) - & +dexp(v(t,ii,iib,iparm)+entfac(t)) + & +dexp(v(t,ii,iib,iparm)+entfac(t)-fi_min(ii,iib,iparm)) enddo #endif enddo ! ii @@ -432,10 +494,12 @@ c write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft enddo enddo #endif +#ifdef DEBUG write (iout,*) "REDUCE size",maxR,MaxT_h,nParmSet, & maxR*MaxT_h*nParmSet write (iout,*) "MPI_COMM_WORLD",MPI_COMM_WORLD, & " WHAM_COMM",WHAM_COMM +#endif call MPI_Reduce(fi_p(1,1,1),fi(1,1,1),maxR*MaxT_h*nParmSet, & MPI_DOUBLE_PRECISION, & MPI_SUM,Master,WHAM_COMM,IERROR) @@ -455,7 +519,7 @@ c write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft do iparm=1,nParmSet do ib=1,nT_h(iparm) do i=1,nR(ib,iparm) - fi(i,ib,iparm)=-dlog(fi(i,ib,iparm)) + fi(i,ib,iparm)=-dlog(fi(i,ib,iparm))-fi_min(i,ib,iparm) avefi=avefi+fi(i,ib,iparm) enddo enddo @@ -674,7 +738,6 @@ C Determine the minimum energes for all parameter sets and temperatures enddo write (iout,*) "potEmin_min",potEmin_min #endif -#undef DEBUG #ifdef MPI do t=0,tmax